Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA.
Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA.
Nat Commun. 2017 Apr 28;8:15024. doi: 10.1038/ncomms15024.
Nucleic acid editing enzymes are essential components of the immune system that lethally mutate viral pathogens and somatically mutate immunoglobulins, and contribute to the diversification and lethality of cancers. Among these enzymes are the seven human APOBEC3 deoxycytidine deaminases, each with unique target sequence specificity and subcellular localization. While the enzymology and biological consequences have been extensively studied, the mechanism by which APOBEC3s recognize and edit DNA remains elusive. Here we present the crystal structure of a complex of a cytidine deaminase with ssDNA bound in the active site at 2.2 Å. This structure not only visualizes the active site poised for catalysis of APOBEC3A, but pinpoints the residues that confer specificity towards CC/TC motifs. The APOBEC3A-ssDNA complex defines the 5'-3' directionality and subtle conformational changes that clench the ssDNA within the binding groove, revealing the architecture and mechanism of ssDNA recognition that is likely conserved among all polynucleotide deaminases, thereby opening the door for the design of mechanistic-based therapeutics.
核酸编辑酶是免疫系统的重要组成部分，它们能使病毒病原体致命突变，并使免疫球蛋白体细胞突变，从而促进癌症的多样化和致命性。在这些酶中，有七种人类 APOBEC3 脱氨酶，每种酶都具有独特的靶序列特异性和亚细胞定位。尽管这些酶的酶学和生物学特性已经得到了广泛的研究，但 APOBEC3 识别和编辑 DNA 的机制仍然难以捉摸。在这里，我们展示了一个与 ssDNA 结合在活性位点的胞嘧啶脱氨酶复合物的晶体结构，分辨率为 2.2Å。该结构不仅可视化了 APOBEC3A 进行催化的活性位点，还确定了赋予对 CC/TC 基序特异性的残基。APOBEC3A-ssDNA 复合物定义了 5'-3' 方向性和细微的构象变化，使 ssDNA 在内结合槽中紧密结合，揭示了 ssDNA 识别的结构和机制，该机制可能在所有多核苷酸脱氨酶中都保守，从而为基于机制的治疗药物的设计打开了大门。
